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3hrd

From Proteopedia

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Current revision

Crystal structure of nicotinate dehydrogenase

Structural highlights

3hrd is a 8 chain structure with sequence from Eubacterium barkeri. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Ligands:	, , , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NDLMS_EUBBA Catalyzes the hydroxylation of nicotinate to 6-hydroxynicotinate. Also active against 2-pyrazinecarboxylic acid, but inactive against other nicotinate analogs.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Nicotinate dehydrogenase (NDH) from Eubacterium barkeri is a molybdoenzyme catalyzing the hydroxylation of nicotinate to 6-hydroxynicotinate. Reactivity of NDH critically depends on the presence of labile (nonselenocysteine) selenium with an as-yet-unidentified form and function. We have determined the crystal structure of NDH and analyzed its active site by multiple wavelengths anomalous dispersion methods. We show that selenium is bound as a terminal Mo=Se ligand to molybdenum and that it occupies the position of the terminal sulfido ligand in other molybdenum hydroxylases. The role of selenium in catalysis has been assessed by model calculations, which indicate an acceleration of the critical hydride transfer from the substrate to the selenido ligand in the course of substrate hydroxylation when compared with an active site containing a sulfido ligand. The MoO(OH)Se active site of NDH shows a novel type of utilization and reactivity of selenium in nature.

The Mo-Se active site of nicotinate dehydrogenase.,Wagener N, Pierik AJ, Ibdah A, Hille R, Dobbek H Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11055-60. Epub 2009 Jun 22. PMID:19549881^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Gladyshev VN, Khangulov SV, Stadtman TC. Properties of the selenium- and molybdenum-containing nicotinic acid hydroxylase from Clostridium barkeri. Biochemistry. 1996 Jan 9;35(1):212-23. PMID:8555176 doi:http://dx.doi.org/10.1021/bi951793i
↑ Wagener N, Pierik AJ, Ibdah A, Hille R, Dobbek H. The Mo-Se active site of nicotinate dehydrogenase. Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11055-60. Epub 2009 Jun 22. PMID:19549881

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3hrd"

@@ Line 1: / Line 1: @@
 ==Crystal structure of nicotinate dehydrogenase==
-<StructureSection load='3hrd' size='340' side='right' caption='[[3hrd]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='3hrd' size='340' side='right'caption='[[3hrd]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3hrd]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Eubacterium_barkeri Eubacterium barkeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HRD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3hrd]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Eubacterium_barkeri Eubacterium barkeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HRD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MCN:PTERIN+CYTOSINE+DINUCLEOTIDE'>MCN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MOS:DIOXOTHIOMOLYBDENUM(VI)+ION'>MOS</scene>, <scene name='pdbligand=NIO:NICOTINIC+ACID'>NIO</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=SE:SELENIUM+ATOM'>SE</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3hrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hrd OCA], [http://pdbe.org/3hrd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hrd RCSB], [http://www.ebi.ac.uk/pdbsum/3hrd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hrd ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MCN:PTERIN+CYTOSINE+DINUCLEOTIDE'>MCN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MOS:DIOXOTHIOMOLYBDENUM(VI)+ION'>MOS</scene>, <scene name='pdbligand=NIO:NICOTINIC+ACID'>NIO</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=SE:SELENIUM+ATOM'>SE</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3hrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hrd OCA], [https://pdbe.org/3hrd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hrd RCSB], [https://www.ebi.ac.uk/pdbsum/3hrd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hrd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NDSFS_EUBBA NDSFS_EUBBA]] Catalyzes the hydroxylation of nicotinate to 6-hydroxynicotinate. Also active against 2-pyrazinecarboxylic acid, but inactive against other nicotinate analogs.<ref>PMID:8555176</ref>  [[http://www.uniprot.org/uniprot/NDLMS_EUBBA NDLMS_EUBBA]] Catalyzes the hydroxylation of nicotinate to 6-hydroxynicotinate. Also active against 2-pyrazinecarboxylic acid, but inactive against other nicotinate analogs.<ref>PMID:8555176</ref>  [[http://www.uniprot.org/uniprot/NDFS_EUBBA NDFS_EUBBA]] Catalyzes the hydroxylation of nicotinate to 6-hydroxynicotinate. Also active against 2-pyrazinecarboxylic acid, but inactive against other nicotinate analogs.<ref>PMID:8555176</ref>  [[http://www.uniprot.org/uniprot/NDMMS_EUBBA NDMMS_EUBBA]] Catalyzes the hydroxylation of nicotinate to 6-hydroxynicotinate. Also active against 2-pyrazinecarboxylic acid, but inactive against other nicotinate analogs.<ref>PMID:8555176</ref>
+[https://www.uniprot.org/uniprot/NDLMS_EUBBA NDLMS_EUBBA] Catalyzes the hydroxylation of nicotinate to 6-hydroxynicotinate. Also active against 2-pyrazinecarboxylic acid, but inactive against other nicotinate analogs.<ref>PMID:8555176</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 34: @@
 </StructureSection>
 [[Category: Eubacterium barkeri]]
-[[Category: Dobbek, H]]
+[[Category: Large Structures]]
-[[Category: Hille, R]]
+[[Category: Dobbek H]]
-[[Category: Pierik, A J]]
+[[Category: Hille R]]
-[[Category: Wagener, N]]
+[[Category: Pierik AJ]]
-[[Category: 2fe-2]]
+[[Category: Wagener N]]
-[[Category: Iron]]
-[[Category: Iron-sulfur]]
-[[Category: Metal-binding]]
-[[Category: Oxidoreductase]]
-[[Category: Selenium ligand]]

3hrd

From Proteopedia

Current revision

Crystal structure of nicotinate dehydrogenase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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